Issue 876 and more. #885
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Issue 876 and more. #885
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…there missing... (Note, PC/Paxtools now generates shorter sbgn-ml xml IDs, easier to parse and map back to original PC biopax URIs...)
…X URIs; not done!.. Note, PC/Paxtools from now will generate shorter sbgn-ml IDs, easier to parse back to original PC URIs.
absolute BioPAX URIs are now CyJson node ids or at least prefix of those (followed by '_someMd5sum' value or '_LEFTTORIGHT' or alike); it's easy to map nodes to biopax elements now. In the future, all or most of biopax and other/summary metadata could come inside the SBGN-ML result (to be gnerated by the Paxtools java sbgn-converter and stored in Notes, Extensions elements as it was supposed to by SBGN-ML design... Looks, we soon will get rid of the graph metadata tables in the rethinkdb and additional (after sbgn data) queries for biopax properties and jsonld model!
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Works fine (see appsbeta.pathwaycommons.org and yeast.pathwaycommons.org) |
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This also depends on Paxtools/sbgn-converter changes (generation of xml ids) and cpath2 (once rebuilt,restarted.)
Code is cleaner now and should work with yeast, beta PC2 servers as well (if you run the app with correct PC_URL, updated generic entities to gene names map, and empty rethinkdb.)
Ah, and PC_XMLBASE option is probably not required at all anymore (I'll check and remove it soon.)
Before everyone can test this PR, I need to restart beta.- and yeast.pathwaycommons.org/pc2/